| Integrative proteomic profiling reveals PRC2-dependent epigenetic crosstalk maintains ground-state pluripotency G Van Mierlo, RAM Dirks, L De Clerck, AB Brinkman, M Huth, SL Kloet, ... Cell stem cell 24 (1), 123-137. e8, 2019 | 107 | 2019 |
| Rapid and in-depth coverage of the (phospho-) proteome with deep libraries and optimal window design for dia-PASEF P Skowronek, M Thielert, E Voytik, MC Tanzer, FM Hansen, S Willems, ... Molecular & Cellular Proteomics, 100279, 2022 | 82 | 2022 |
| AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics WF Zeng, XX Zhou, S Willems, C Ammar, M Wahle, I Bludau, E Voytik, ... Nature Communications 13 (1), 7238, 2022 | 81 | 2022 |
| The structural context of posttranslational modifications at a proteome-wide scale I Bludau, S Willems, WF Zeng, MT Strauss, FM Hansen, MC Tanzer, ... PLoS biology 20 (5), e3001636, 2022 | 77 | 2022 |
| Statistical framework for detection of genetically modified organisms based on next generation sequencing S Willems, MA Fraiture, D Deforce, SCJ De Keersmaecker, M De Loose, ... Food chemistry 192, 788-798, 2016 | 66 | 2016 |
| Proteins involved in embryo-maternal interaction around the signalling of maternal recognition of pregnancy in the horse K Smits, S Willems, K Van Steendam, M Van De Velde, V De Lange, ... Scientific reports 8 (1), 5249, 2018 | 58 | 2018 |
| Removing the hidden data dependency of DIA with predicted spectral libraries B Van Puyvelde, S Willems, R Gabriels, S Daled, L De Clerck, ... Proteomics 20 (3-4), 1900306, 2020 | 54 | 2020 |
| Forensic tri-allelic SNP genotyping using nanopore sequencing S Cornelis, Y Gansemans, AS Vander Plaetsen, J Weymaere, S Willems, ... Forensic Science International: Genetics 38, 204-210, 2019 | 44 | 2019 |
| Tackling aspecific side reactions during histone propionylation: The promise of reversing overpropionylation P Meert, S Dierickx, E Govaert, L De Clerck, S Willems, M Dhaenens, ... Proteomics 16 (14), 1970-1974, 2016 | 36 | 2016 |
| AlphaPept: a modern and open framework for MS-based proteomics MT Strauss, I Bludau, WF Zeng, E Voytik, C Ammar, JP Schessner, ... Nature Communications 15 (1), 2168, 2024 | 35 | 2024 |
| Cov-MS: a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients B Van Puyvelde, K Van Uytfanghe, O Tytgat, L Van Oudenhove, ... Jacs Au 1 (6), 750-765, 2021 | 35 | 2021 |
| Comparison of fractionation proteomics for local SWATH library building E Govaert, K Van Steendam, S Willems, L Vossaert, M Dhaenens, ... Proteomics 17 (15-16), 1700052, 2017 | 33 | 2017 |
| Synchro-PASEF allows precursor-specific fragment ion extraction and interference removal in data-independent acquisition P Skowronek, F Krohs, M Lubeck, G Wallmann, ECM Itang, P Koval, ... Molecular & Cellular Proteomics 22 (2), 2023 | 32 | 2023 |
| Extracting histones for the specific purpose of label‐free MS E Govaert, K Van Steendam, E Scheerlinck, L Vossaert, P Meert, M Stella, ... Proteomics 16 (23), 2937-2944, 2016 | 29 | 2016 |
| A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics B Van Puyvelde, S Daled, S Willems, R Gabriels, A Gonzalez de Peredo, ... Scientific Data 9 (1), 126, 2022 | 27 | 2022 |
| AlphaTims: Indexing Trapped Ion Mobility Spectrometry–TOF Data for Fast and Easy Accession and Visualization S Willems, E Voytik, P Skowronek, MT Strauss, M Mann Molecular & Cellular Proteomics 20, 2021 | 26 | 2021 |
| Untargeted histone profiling during naive conversion uncovers conserved modification markers between mouse and human L De Clerck, J Taelman, M Popovic, S Willems, M Van der Jeught, ... Scientific reports 9 (1), 17240, 2019 | 21 | 2019 |
| hSWATH: Unlocking SWATH’s full potential for an untargeted histone perspective L De Clerck, S Willems, R Noberini, C Restellini, B Van Puyvelde, ... Journal of Proteome Research 18 (11), 3840-3849, 2019 | 21 | 2019 |
| Flagging False Positives Following Untargeted LC–MS Characterization of Histone Post-Translational Modification Combinations S Willems, M Dhaenens, E Govaert, L De Clerck, P Meert, C Van Neste, ... Journal of Proteome Research 16 (2), 655-664, 2017 | 19 | 2017 |
| Comprehensive histone epigenetics: A mass spectrometry based screening assay to measure epigenetic toxicity S Verhelst, L De Clerck, S Willems, B Van Puyvelde, S Daled, D Deforce, ... MethodsX 7, 101055, 2020 | 15 | 2020 |
